Setting up Mainstage with two controllers using seperate MIDI channels

I'm starting from scratch and migrating from a hardware system to Mainstage. Ultimately I would like to use two controllers on separate MIDI channels utilizing multiple outputs on my audio interface. Once that is set, I would like to have OnSong on my iPad change MS patches so I don't need the Mac in front of me. I'm also fairly new to the Mac world from PC life. My audio interface is a MOTU Ultralite MK5.

[Re-Titled by Moderator]

Original Title: Mainstage for beginners